This work was funded by the ECO-SERVE project through the 2013–2014 BiodivERsA/FACCE‐JPI joint call for research proposals, with the national funders ANR, NWO, FCT (BiodivERsA/001/2014), MINECO, FORMAS and SNF. Eduardo Nascimento was supported by CNPq – Brazil (CNPq Fellowship Holder – Brazil). The authors would like to thank to Filipe Carvalho for helping in the maintenance of the mesocosm experiment. Thanks to Cindy Arnoldi for help with chemical and enzymatic analyses. We are greatly indebted to the owners of the different farms from where the TMEs were collected. Thank goes to the Genome Quebec Innovation Center (Montreal, Canada) for excellent support and execution of Illumina sequencing. The DOK trial from which the Swiss TMEs were extracted is funded by the Swiss Federal Office of Agriculture. The bioinformatics support of the BMBF-funded project Bielefeld-Gießen Center for Microbial Bioinformatics—BiGi (grant 031A533) within the German Network for Bioinformatics Infrastructure (de.NBI) is gratefully acknowledged.